Abstract
We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics.
Highlights
Swamp eel (Monopterus albus) taxonomically belongs to teleosts, the family Synbranchidae of the order Synbranchiformes (Neoteleostei, Teleostei, and Vertebrata)
Analysis of physical location and density of microsatellites on the chromosomes showed that distribution of microsatellites across the chromosomes was uniform with regard to a certain motif type, whereas there were variable densities in different microsatellite types across the chromosomes, for example, 112.56–149.02/Mb in dinucleotides, 22.38–27.17/Mb in trinucleotides, 7.51–9.49/Mb in tetranucleotides, 1.79–2.60/Mb in pentanucleotides, and 0.07–0.26/Mb in hexanucleotides (Fig.1e)
Microsatellites that are widely distributed in a genome are important genetic markers for assessing genetic diversity, genetic map construction, comparative genomics, and marker-assisted selection breeding
Summary
Swamp eel (Monopterus albus) taxonomically belongs to teleosts, the family Synbranchidae of the order Synbranchiformes (Neoteleostei, Teleostei, and Vertebrata). Microsatellites are observed in almost all known eukaryotic and prokaryotic genomes, and present in both coding and non-coding regions[3,4,5]. This makes microsatellite a powerful genetic marker for a variety of applications, such as genetic linkage mapping, population genetics, QTL (quantitative trait loci)-based selection breeding, molecular breeding, and evolutionary studies[6,7,8,9,10]. A few of SSR markers in swamp eel have been reported[22,23,24], a genome-wide characterization of microsatellites remains to be identified in this species. The novel set of microsatellites in swamp eel provides a valuable dataset for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics
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